High occurrence of jellyfish predation by black-browed and Campbell albatross identified by DNA metabarcoding

A belly full of jelly? DNA metabarcoding shows evidence for gelatinous zooplankton predation by several fish species in Greenland waters

The waters of Greenland harbour a high species richness and biomass of gelatinous zooplankton (GZP); however, their role in the diet of the many fish species, including commercially exploited species, has not yet been verified. Traditionally, GZP was considered to be a trophic dead end, i.e. with a limited contribution as prey for higher trophic levels. We applied DNA metabarcoding of two gene fragments (COI, 18S V1-V2) to the stomach contents of seven pelagic and demersal fish species in Greenland waters, to identify their prey composition as well as the occurrence of GZP predation. We detected GZP DNA reads in the stomachs of all investigated fish species, with frequency of occurrences ranging from 12.5% (for Melanogrammus aeglefinus) to 50% (for Argentina silus). GZP predation had not yet been reported for several of these species. GZP were found to majorly contribute to the diet of A. silus and Anarhichas denticulatus, particularly, the siphonophore Nanomia cara and the scyphozoan Atolla were of a high importance as prey, respectively. The use of multiple genetic markers enabled us to detect a total of 59 GZP taxa in the fish stomachs with several GZP species being detected only by one of the markers.

Trophic plasticity of a tropical seabird revealed through DNA metabarcoding and stable isotope analyses

DNA metabarcoding and stable isotope analysis have significantly advanced our understanding of marine trophic ecology, aiding systematic research on foraging habits and species conservation. In this study, we employed these methods to analyse faecal and blood samples, respectively, to compare the trophic ecology of two Red-billed Tropicbird (Phaethonaethereus; Linnaeus, 1758) colonies on Mexican islands in the Pacific. Trophic patterns among different breeding stages were also examined at both colonies. Dietary analysis reveals a preference for epipelagic fish, cephalopods, and small crustaceans, with variations between colonies and breeding stages. Isotopic values (δ15N and δ13C) align with DNA metabarcoding results, with wider niches during incubation stages. Differences in diet are linked to environmental conditions and trophic plasticity among breeding stages, influenced by changing physiological requirements and prey availability. Variations in dietary profiles reflect contrasting environmental conditions affecting local prey availability.

Physiological and transcriptomic responses of Aurelia coerulea polyps to acidified seawater conditions

Scyphozoan jellyfish, known for their evolutionary position and ecological significance, are thought to exhibit relatively notable resilience to ocean acidification. However, knowledge regarding the molecular mechanisms underlying the scyphozoan jellyfish response to acidified seawater conditions is currently lacking. In this study, two independent experiments were conducted to determine the physiological and molecular responses of moon jellyfish (Aurelia coerulea) polyps to within- and trans-generational exposure to two reduced pH treatments (pH 7.8 and pH 7.6). The results revealed that the asexual reproduction of A. coerulea polyps significantly declined under acute exposure to pH 7.6 compared with that of polyps at ambient pH conditions. Transcriptomics revealed a notable upregulation of genes involved in immunity and cytoskeleton components. In contrast, genes associated with metabolism were downregulated in response to reduced pH treatments after 6 weeks of within-generational acidified conditions. However, reduced pH treatments had no significant influence on the asexual reproduction of A. coerulea polyps after exposure to acidified conditions over a total of five generations, suggesting that A. coerulea polyps may acclimate to low pH levels. Transcriptomics revealed distinct gene expression profiles between within- and trans-generational exposure groups to two reduced pH treatments. The offspring polyps of A. coerulea subjected to trans-generational acidified conditions exhibited both upregulated and downregulated expression of genes associated with metabolism. These physiological and transcriptomic characteristics of A. coerulea polyps in response to elevated CO2 levels suggest that polyps produced asexually under acidified conditions may be resilient to such conditions in the future.

Biodiversity and distribution patterns of blooming jellyfish in the Bohai Sea revealed by eDNA metabarcoding

BACKGROUND

The mass occurrence of scyphozoan jellyfish severely affects marine ecosystems and coastal economies, and the study of blooming jellyfish population dynamics has emerged in response. However, traditional ecological survey methods required for such research have difficulties in detecting cryptic life stages and surveying population dynamics owing to high spatiotemporal variations in their occurrence. The environmental DNA (eDNA) technique is an effective tool for overcoming these limitations.

RESULTS

In this study, we investigated the biodiversity and spatial distribution characteristics of blooming jellyfish in the Bohai Sea of China using an eDNA metabarcoding approach, which covered the surface, middle, and bottom seawater layers, and sediments. Six jellyfish taxa were identified, of which Aurelia coerulea, Nemopilema nomurai, and Cyanea nozakii were the most dominant. These three blooming jellyfish presented a marked vertical distribution pattern in the offshore regions. A. coerulea was mainly distributed in the surface layer, whereas C. nozakii and N. nomurai showed a upper-middle and middle-bottom aggregation, respectively. Horizontally, A. coerulea and C. nozakii were more abundant in the inshore regions, whereas N. nomurai was mainly distributed offshore. Spearman's correlation analysis revealed a strong correlation between the eDNA of the three dominant blooming jellyfish species and temperature, salinity, and nutrients.

CONCLUSIONS

Our study confirms the applicability of the eDNA approach to both biodiverstiy evaluation of blooming jellyfish and investigating their spatial distribution, and it can be used as a supplementary tool to traditional survey methods.

An invasive appetite: Combining molecular and stable isotope analyses to reveal the diet of introduced house mice (Mus musculus) on a small, subtropical island

House mice (Mus musculus) pose a conservation threat on islands, where they adversely affect native species' distributions, densities, and persistence. On Sand Island of Kuaihelani, mice recently began to depredate nesting adult mōlī (Laysan Albatross, Phoebastria immutabilis). Efforts are underway to eradicate mice from Sand Island, but knowledge of mouse diet is needed to predict ecosystem response and recovery following mouse removal. We used next-generation sequencing to identify what mice eat on Sand Island, followed by stable isotope analysis to estimate the proportions contributed by taxa to mouse diet. We collected paired fecal and hair samples from 318 mice between April 2018 to May 2019; mice were trapped approximately every eight weeks among four distinct habitat types to provide insight into temporal and spatial variation. Sand Island's mice mainly consume arthropods, with nearly equal (but substantially smaller) contributions of C3 plants, C4 plants, and mōlī. Although seabird tissue is a small portion of mouse diet, mice consume many detrital-feeding arthropods in and around seabird carcasses, such as isopods, flesh flies, ants, and cockroaches. Additionally, most arthropods and plants eaten by mice are non-native. Mouse diet composition differs among habitat types but changes minimally throughout the year, indicating that mice are not necessarily limited by food source availability or accessibility. Eradication of house mice may benefit seabirds on Sand Island (by removing a terrestrial, non-native predator), but it is unclear how arthropod and plant communities may respond and change. Non-native and invasive arthropods and plants previously consumed (and possibly suppressed) by mice may be released post-eradication, which could prevent recovery of native taxa. Comprehensive knowledge of target species' diet is a critical component of eradication planning. Dietary information should be used both to identify and to monitor which taxa may respond most strongly to invasive species removal and to assess if proactive, pre-eradication management activities are warranted.

Intrinsic and extrinsic drivers of shape variation in the albatross compound bill

Albatross are the largest seabirds on Earth and have a suite of adaptations for their pelagic lifestyle. Rather than having a bill made of a single piece of keratin, Procellariiformes have a compound rhamphotheca, made of several joined plates. Drivers of the shape of the albatross bill have not been explored. Here we use three-dimensional scans of 61 upper bills from 12 species of albatross to understand whether intrinsic (species assignment & size) or extrinsic (diet) factors predict bill shape. Diet is a significant predictor of bill shape with coarse dietary categories providing higher R2 values than dietary proportion data. We also find that of the intrinsic factors, species assignment accounts for ten times more of the variation than size (72% versus 6.8%) and that there is a common allometric vector of shape change between all species. When considering species averages in a phylogenetic framework, there are significant Blomberg's K results for both shape and size (K = 0.29 & 1.10) with the first axis of variation having a much higher K value (K = 1.9), reflecting the split in shape at the root of the tree. The influence of size on bill shape is limited, with species assignment and diet predicting far more of the variation. The results show that both intrinsic and extrinsic factors are needed to understand morphological evolution.

Otterly delicious: Spatiotemporal variation in the diet of a recovering population of Eurasian otters (Lutra lutra) revealed through DNA metabarcoding and morphological analysis of prey remains

Eurasian otters are apex predators of freshwater ecosystems and a recovering species across much of their European range; investigating the dietary variation of this predator over time and space, therefore, provides opportunities to identify changes in freshwater trophic interactions and factors influencing the conservation of otter populations. Here we sampled feces from 300 dead otters across England and Wales between 2007 and 2016, conducting both morphological analyses of prey remains and dietary DNA metabarcoding. Comparison of these methods showed that greater taxonomic resolution and breadth could be achieved using DNA metabarcoding but combining data from both methodologies gave the most comprehensive dietary description. All otter demographics exploited a broad range of taxa and variation likely reflected changes in prey distributions and availability across the landscape. This study provides novel insights into the trophic generalism and adaptability of otters across Britain, which is likely to have aided their recent population recovery, and may increase their resilience to future environmental changes.

The Falkland Islands marine ecosystem: A review of the seasonal dynamics and trophic interactions across the food web

The Falkland Islands marine environment host a mix of temperate and subantarctic species. This review synthesizes baseline information regarding ontogenetic migration patterns and trophic interactions in relation to oceanographic dynamics of the Falkland Shelf, which is useful to inform ecosystem modelling. Many species are strongly influenced by regional oceanographic dynamics that bring together different water masses, resulting in high primary production which supports high biomass in the rest of the food web. Further, many species, including those of commercial interest, show complex ontogenetic migrations that separate spawning, nursing, and feeding grounds spatially and temporally, producing food web connections across space and time. The oceanographic and biological dynamics may make the ecosystem vulnerable to climatic changes in temperature and shifts in the surrounding area. The Falkland marine ecosystem has been understudied and various functional groups, deep-sea habitats and inshore-offshore connections are poorly understood and should be priorities for further research.

Development of a multiprimer metabarcoding approach to understanding trophic interactions in agroecosystems

To understand trophic interactions and the precise ecological role of each predatory species, it is important to know which arthropod and plant resources are used by generalist predators in agroecosystems. Molecular approaches, such as the use of high-throughput sequencing (HTS), play a key role in identifying these resources. This study develops a multiprimer metabarcoding approach for screening the most common trophic interactions of two predatory arthropods with contrasting morphologies, Rhagonycha fulva (Coleoptera: Cantharidae) and Anthocoris nemoralis (Hemiptera: Anthocoridae) collected from a peach crop. To reduce the time and cost of this metabarcoding approach, we first evaluated the effect of using two different predator-pools of different size (10 and 23 individuals of the same species). We also used our system to analyze the performance of one and two primer pairs in the same library. Our results show that the analysis of 23 individuals together with the use of two primer pairs in the same library optimize the HTS analysis. Using these best-performing conditions, we then analyzed the entire bodies of field-collected predators as well as the washing solutions used to clean the insect bodies. We were able to identify both gut content (i.e., diet) and external pollen load (i.e., on the insects' bodies). This study also demonstrates the importance of washing predatory insects' bodies prior to HTS analysis when the target species have a considerable size (>10 mm) and hairy structures. This metabarcoding approach has significant potential for the study of trophic links in agriculture, revealing expected and unexpected trophic relationships.

Characterizing the secret diets of siphonophores (Cnidaria: Hydrozoa) using DNA metabarcoding

Siphonophores (Cnidaria: Hydrozoa) are abundant and diverse gelatinous predators in open-ocean ecosystems. Due to limited access to the midwater, little is known about the diets of most deep-dwelling gelatinous species, which constrains our understanding of food-web structure and nutrient flow in these vast ecosystems. Visual gut-content methods can rarely identify soft-bodied rapidly-digested prey, while observations from submersibles often overlook small prey items. These methods have been differentially applied to shallow and deep siphonophore taxa, confounding habitat and methodological biases. DNA metabarcoding can be used to assess both shallow and deep species' diets under a common methodological framework, since it can detect both small and gelatinous prey. We (1) further characterized the diets of open-ocean siphonophores using DNA metabarcoding, (2) compared the prey detected by visual and molecular methods to evaluate their technical biases, and (3) evaluated tentacle-based predictions of diet. To do this, we performed DNA metabarcoding analyses on the gut contents of 39 siphonophore species across depths to describe their diets, using six barcode regions along the 18S gene. Taxonomic identifications were assigned using public databases combined with local zooplankton sequences. We identified 55 unique prey items, including crustaceans, gelatinous animals, and fish across 47 siphonophore specimens in 24 species. We reported 29 novel predator-prey interactions, among them the first insights into the diets of nine siphonophore species, many of which were congruent with the dietary predictions based on tentilla morphology. Our analyses detected both small and gelatinous prey taxa underrepresented by visual methods in species from both shallow and deep habitats, indicating that siphonophores play similar trophic roles across depth habitats. We also reveal hidden links between siphonophores and filter-feeders near the base of the food web. This study expands our understanding of the ecological roles of siphonophores in the open ocean, their trophic roles within the 'jelly-web', and the importance of their diversity for nutrient flow and ecosystem functioning. Understanding these inconspicuous yet ubiquitous predator-prey interactions is critical to predict the impacts of climate change, overfishing, and conservation policies on oceanic ecosystems.

Unexpectedly deep diving in an albatross

Albatrosses are the iconic aerial wanderers of the oceans, supremely adapted for long-distance dynamic soaring flight. Perhaps because of this they are considered poorly adapted for diving¹, in contrast to many smaller shearwater and petrel relatives, despite having amphibious eyes², and an a priori mass advantage for oxygen-storage tolerance³. Modern biologging studies have largely confirmed this view^4,5, casting doubt on earlier observations using capillary tube maximum depth gauges¹, which may exaggerate depths, and emphasising albatrosses' reliance on near-surface feeding. Nevertheless, uncertainty about albatross diving remains an important knowledge gap since bycatch in human fisheries (e.g. birds becoming hooked when diving for longline bait fish) is thought to be driving many population declines in this most threatened group of birds⁶. Here we show, using miniature electronic depth loggers (TDRs), that black-browed albatross, Thalassarche melanophris, can dive to much greater depths (19 m) and for much longer (52 s) than previously thought - three times the maxima previously recorded for this species (6 m and 15 s), and more than twice the maxima reliably recorded previously for any albatross (from 113.7 bird-days of tracking^4,5,7). Further evidence that diving may be a significant behavioural adaptation in some albatrosses comes from co-deployed 3-axis accelerometers showing that these deeper dives, which occur in most individuals we tracked, involve active under-water propulsion without detectable initial assistance from momentum, sometimes with bottom phases typical of active prey pursuit. Furthermore, we find (from co-deployed GPS) that diving occurs primarily in the distal portions of long-distance foraging trips, with deeper dives occurring exclusively during daylight or civil twilight, confirming the importance of visual guidance.

DNA-metabarcoding reveals the importance of gelatinous zooplankton in the diet of Pandalus borealis, a keystone species in the Arctic

Information about the dietary composition of a species is crucial to understanding their position and role in the food web. Increasingly molecular approaches such as DNA-metabarcoding are used in studying trophic relations, not least because they may alleviate problems such as low taxonomic resolution or underestimation of digestible taxa in the diet. Here, we used DNA-metabarcoding with universal primers for cytochrome c oxidase I (COI), to study the diet composition of the Northern shrimp (Pandalus borealis), an Arctic keystone species with large socio-economic importance. Across locations, jellyfish and chaetognaths were the most important components in the diet of P. borealis, jointly accounting for 40-60% of the total read abundance. This dietary importance of gelatinous zooplankton contrasts sharply with published results based on SCA. At the same time, diet composition differed between fjord and shelf locations, pointing to different food webs supporting P. borealis in these two systems. Our study underscores the potential of molecular approaches to provide new insights into the diet of marine invertebrates that are difficult to obtain with traditional methods, and calls for a revision of the role of gelatinous zooplankton in the diet of the key Arctic species P. borealis, and in extension, Arctic food webs.

Metabarcoding confirms the opportunistic foraging behaviour of Atlantic bluefin tuna and reveals the importance of gelatinous prey

Studies of the diet, feeding habits and trophic activity of top marine predators are essential for understanding their trophodynamics. The main direct method used for such studies thus far has been morphological inventories of stomach contents. This approach presents limitations such as missing gelatinous prey, which are usually digested too quickly to be detectable. Here, we analysed the stomachs of 48 Atlantic bluefin tuna (Thunnus thynnus, approximately 15 to 60 kg, including juveniles and adult fishes) collected from the Mediterranean Sea through the metabarcoding of two gene regions (cytochrome c oxidase subunit I (COI) and the ribosomal 18S-V1V2 region). The identified prey taxa and their relative read abundances (RRAs) estimated using COI results were in line with the findings of morphologically based inventories simultaneously performed on the same set of tuna samples. In both cases (and with the same rankings), the prey taxa included anchovy (Engraulis encrasicolus, here detected in more than 80% of samples, RRA = 43%), sardine (Sardina pilchardus, also approximately 80%, RRA = 30%), sprat (Sprattus sprattus, approximately 66%, RRA = 8%), mackerel (Scomber colias, approximately 44%, RRA = 7%) and cephalopods (approximately 15%, RRA = 1.4%). Another striking result was the detection, based on 18S (with which vertebrates were detected as the most abundant group, RRA = 61.6%), of a high prevalence and diversity of gelatinous organisms (RRA = 27.1%), including cnidarians (6.7%), salps (11.7%), and ctenophores (8.7%), the latter increasing with the size of the predator. These results thus support the hypothesis of the role of gelatinous prey in the diet of Atlantic bluefin tuna, suggesting that this species is even more generalist and opportunistic than previously thought. This study further confirms that DNA metabarcoding can be a powerful tool for assessing the diet and trophodynamics of top marine predators.

All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment

Monitoring marine resource exploitation is a key activity in fisheries science and biodiversity conservation. Since research surveys are time consuming and costly, fishery-dependent data (i.e., derived directly from fishing vessels) are increasingly credited with a key role in expanding the reach of ocean monitoring. Fishing vessels may be seen as widely ranging data-collecting platforms, which could act as a fleet of sentinels for monitoring marine life, in particular exploited stocks. Here, we investigate the possibility of assessing catch composition of single hauls carried out by trawlers by applying DNA metabarcoding to the dense water draining from fishing nets just after the end of hauling operations (hereafter "slush"). We assess the performance of this approach in portraying β-diversity and examining the quantitative relationship between species abundances in the catch and DNA amount in the slush (read counts generated by amplicon sequencing). We demonstrate that the assemblages identified using DNA in the slush satisfactorily mirror those returned by visual inspection of net content (about 71% of species and 86% of families of fish) and detect a strong relationship between read counts and species abundances in the catch. We therefore argue that this approach could be upscaled to serve as a powerful source of information on the structure of demersal assemblages and the impact of fisheries.

All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment

Monitoring marine resource exploitation is a key activity in fisheries science and biodiversity conservation. Since research surveys are time consuming and costly, fishery-dependent data (i.e., derived directly from fishing vessels) are increasingly credited with a key role in expanding the reach of ocean monitoring. Fishing vessels may be seen as widely ranging data-collecting platforms, which could act as a fleet of sentinels for monitoring marine life, in particular exploited stocks. Here, we investigate the possibility of assessing catch composition of single hauls carried out by trawlers by applying DNA metabarcoding to the dense water draining from fishing nets just after the end of hauling operations (hereafter "slush"). We assess the performance of this approach in portraying β-diversity and examining the quantitative relationship between species abundances in the catch and DNA amount in the slush (read counts generated by amplicon sequencing). We demonstrate that the assemblages identified using DNA in the slush satisfactorily mirror those returned by visual inspection of net content (about 71% of species and 86% of families of fish) and detect a strong relationship between read counts and species abundances in the catch. We therefore argue that this approach could be upscaled to serve as a powerful source of information on the structure of demersal assemblages and the impact of fisheries.

Decades of dietary data demonstrate regional food web structures in the Southern Ocean

Understanding regional-scale food web structure in the Southern Ocean is critical to informing fisheries management and assessments of climate change impacts on Southern Ocean ecosystems and ecosystem services. Historically, a large component of Southern Ocean ecosystem research has focused on Antarctic krill, which provide a short, highly efficient food chain, linking primary producers to higher trophic levels. Over the last 15 years, the presence of alternative energy pathways has been identified and hypotheses on their relative importance in different regions raised. Using the largest circumpolar dietary database ever compiled, we tested these hypotheses using an empirical circumpolar comparison of food webs across the four major regions/sectors of the Southern Ocean (defined as south of 40°S) within the austral summer period. We used network analyses and generalizations of taxonomic food web structure to confirm that while Antarctic krill are dominant as the mid-trophic level for the Atlantic and East Pacific food webs (including the Scotia Arc and Western Antarctic Peninsula), mesopelagic fish and other krill species are dominant contributors to predator diets in the Indian and West Pacific regions (East Antarctica and the Ross Sea). We also highlight how tracking data and habitat modeling for mobile top predators in the Southern Ocean show that these species integrate food webs over large regional scales. Our study provides a quantitative assessment, based on field observations, of the degree of regional differentiation in Southern Ocean food webs and the relative importance of alternative energy pathways between regions.

Similar foraging energetics of two sympatric albatrosses despite contrasting life histories and wind-mediated foraging strategies

Understanding the environmental and behavioral factors that influence how organisms maintain energy balance can inform us about their potential resiliency to rapid environmental changes. Flexibility in maintaining energy balance is particularly important to long-lived, central-place foraging seabirds that are constrained when locating food for offspring in a dynamic ocean environment. To understand the role of environmental interactions, behavioral flexibility and morphological constraints on energy balance, we used doubly labeled water to measure the at-sea daily energy expenditure (DEE) of two sympatrically breeding seabirds, Campbell (Thalassarche impavida) and grey-headed (Thalassarche chrysostoma) albatrosses. We found that species and sexes had similar foraging costs, but DEE varied between years for both species and sexes during early chick rearing in two consecutive seasons. For both species, greater DEE was positively associated with larger proportional mass gain, lower mean wind speeds during water take-offs, greater proportions of strong tailwinds (>12 m s^-1), and younger chick age. Greater proportional mass gains were marginally more costly in male albatrosses that already have higher wing loading. DEE was higher during flights with a greater proportion of strong headwinds for grey-headed albatrosses only. Poleward winds are forecasted to intensify over the next century, which may increase DEE for grey-headed albatrosses that heavily use this region during early chick rearing. Female Campbell albatrosses may be negatively affected by forecasted slackening winds at lower latitudes due to an expected greater reliance on less energy efficient sit-and-wait foraging strategies. Behavioral plasticity associated with environmental variation may influence future population responses to climate change of both species.

Trace elements' reference levels in blood of breeding black-browed albatrosses Thalassarche melanophris from the Falkland Islands

Trace elements' concentration in the ocean is fast growing and is a source of major concern. Being charismatic and at the top of food chains, seabirds are often used as biological monitors of contaminants. We studied the concentration of trace elements in blood of black-browed albatross from the Falklands Islands, which we here show, by tracking with geolocators, forage over most of the Patagonian Shelf. Levels of trace elements were measured in males and females from two different islands. Blood concentrations of trace elements were not significantly different between islands, which is consistent with observations from foraging behavior revealing that birds from both islands foraged in broadly the same areas in the months before sampling. Arsenic and selenium concentrations in females were higher than in males. Sex-related differences in the concentration of these elements may be related to unknown slight differences in diet or to differences in assimilation between sexes. These results provide reference values for monitoring elemental contamination in the Patagonian Shelf Large Marine Ecosystem using black-browed albatrosses, one of the most abundant top predators and a suitable sentinel for the region's environmental health.

Birds suppress pests in corn but release them in soybean crops within a mixed prairie/agriculture system

Birds provide ecosystem services (pest control) in many agroecosystems and have neutral or negative ecological effects (disservices) in others. Large-scale, conventional row crop agriculture is extremely widespread globally, yet few studies of bird effects take place in these agroecosystems. We studied indirect effects of insectivorous birds on corn and soybean crops in fields adjacent to a prairie in Illinois (USA). We hypothesized that prairie birds would forage for arthropods in adjacent crop fields and that the magnitude of services or disservices would decrease with distance from the prairie. We used bird-excluding cages over crops to examine the net effect of birds on corn and soybean grain yield. We also conducted DNA metabarcoding to identify arthropod prey in fecal samples from captured birds. Our exclosure experiments revealed that birds provided net services in corn and net disservices in soybeans. Distance from prairie was not a significant predictor of exclosure treatment effect in either crop. Many bird fecal samples contained DNA from both beneficial arthropods and known economically significant pests of corn, but few economically significant pests of soybeans. Song Sparrows (Melospiza melodia), one of our most captured species, most commonly consumed corn rootworms, an economically significant pest of corn crops. We estimated that birds in this system provided a service worth approximately US $275 ha-1 in corn yield gain, and a disservice valued at approximately $348 ha-1 in soybean yield loss. Our study is the first to demonstrate that birds can provide substantial and economically valuable services in field corn, and disservices in soybean crops. The contrasting findings in the 2 crop systems suggest a range of bird impacts within widespread agroecosystems and demonstrate the importance of quantifying net trophic effects.

Partitioning of diet between species and life history stages of sympatric and cryptic snappers (Lutjanidae) based on DNA metabarcoding

Lutjanus erythropterus and L. malabaricus are sympatric, sister taxa that are important to fisheries throughout the Indo-Pacific. Their juveniles are morphologically indistinguishable (i.e. cryptic). A DNA metabarcoding dietary study was undertaken to assess the diet composition and partitioning between the juvenile and adult life history stages of these two lutjanids. Major prey taxa were comprised of teleosts and crustaceans for all groups except adult L. erythropterus, which instead consumed soft bodied invertebrates (e.g. tunicates, comb jellies and medusae) as well as teleosts, with crustaceans being notably absent. Diet composition was significantly different among life history stages and species, which may be associated with niche habitat partitioning or differences in mouth morphology within adult life stages. This study provides the first evidence of diet partitioning between cryptic juveniles of overlapping lutjanid species, thus providing new insights into the ecological interactions, habitat associations, and the specialised adaptations required for the coexistence of closely related species. This study has improved our understanding of the differential contributions of the juvenile and adult diets of these sympatric species within food webs. The diet partitioning reported in this study was only revealed by the taxonomic resolution provided by the DNA metabarcoding approach and highlights the potential utility of this method to refine the dietary components of reef fishes more generally.

Unravelling the macro-evolutionary ecology of fish-jellyfish associations: life in the 'gingerbread house'

Fish-jellyfish interactions are important factors contributing to fish stock success. Jellyfish can compete with fish for food resources, or feed on fish eggs and larvae, which works to reduce survivorship and recruitment of fish species. However, jellyfish also provide habitat and space for developing larval and juvenile fish which use their hosts as means of protection from predators and feeding opportunities, helping to reduce fish mortality and increase recruitment. Yet, relatively little is known about the evolutionary dynamics and drivers of such associations which would allow for their more effective incorporation into ecosystem models. Here, we found that jellyfish association is a probable adaptive anti-predator strategy for juvenile fish, more likely to evolve in benthic (fish living on the sea floor), benthopelagic (fish living just above the bottom of the seafloor), and reef-associating species than those adapted to other marine habitats. We also found that jellyfish association likely preceded the evolution of a benthic, benthopelagic, and reef-associating lifestyle rather than its evolutionary consequence, as we originally hypothesized. Considering over two-thirds of the associating fish identified here are of economic importance, and the wide-scale occurrence and diversity of species involved, it is clear the formation of fish-jellyfish associations is an important but complex process in relation to the success of fish stocks globally.

Species in the faeces: DNA metabarcoding as a method to determine the diet of the endangered yellow-eyed penguin

Abstract Context. Diet variability is a significant driver of seabird decline; however, data on seabird diet composition and trends have been affected by changes in precision and resolution owing to the evolution of different sampling methods over time. We investigated the effectiveness of applying a passive molecular diet method using faeces obtained from the endangered yellow-eyed penguin. Aims. To assess the feasibility of applying DNA metabarcoding methods to yellow-eyed penguin faeces to evaluate diet, and to compare the reliability of diet results derived from adults and chicks, and from latrine versus fresh faecal samples. Methods. We collected 313 faecal samples from yellow-eyed penguins resident on the Otago coast of New Zealand from October 2016 to August 2017. We used polymerase chain reaction (PCR) with mitochondrial 16S cephalopod and chordate primers to amplify prey DNA present in the faecal samples, and tested the completeness of our assembled reference databases based on previous diet research. Amplified prey DNA sequences were then assigned to taxa from our reference databases by using QIIME2. Key results. Mitochondrial 16S chordate PCR primers were effective at identifying 29 fish taxa, with 98.3% of amplified sequences being identified to species or genus level in 193 samples (61.7% collected). There was no significant difference in the number, occurrence or proportion of ray-finned fish prey DNA sequences derived from fresh samples or latrines. Mitochondrial 16S cephalopod PCR primers classified 1.98% of amplified DNA sequences as targets, with 96.5% of these target sequences being identified to species or genus level in 48 samples (15.3% collected), and five taxa identified. Conclusions. We recommend the collection of latrine samples to enable long-term monitoring of the diet of yellow-eyed penguins, which will optimise the trade-off between wildlife disturbance and dietary resolution. Further refinement is needed to identify cephalopod dietary components for yellow-eyed penguins, because our cephalopod primers were not as specific as those used for ray-finned fishes, amplifying a large number (>98%) of non-cephalopod species. Implications. DNA metabarcoding offers a robust and comprehensive alternative to other, more intrusive, seabird diet-assessment methods, but still requires parallel studies to provide critical information on prey size, true diet composition and diet quality.

Molecular approach indicates consumption of jellyfish by commercially important fish species in a coastal Mediterranean lagoon

Until recently, jellyfish have been ignored as an important source of food, due to their low nutritional value. Here, quantitative PCR was used to detect and quantify the DNA of the jellyfish Aurelia coerulea in the gut contents of commercially important fish species from the Thau Lagoon. Individuals from five fish species were collected during two different periods: the bloom period, when the pelagic stages of A. coerulea are abundant, and the post-bloom period, when only the benthic stage - polyps - is present in the lagoon. The DNA of A. coerulea was detected in the guts of 41.9% of the fish analysed, belonging to four different species. The eel Anguilla anguilla and the seabream Sparus aurata were important jellyfish consumers during the bloom and post-bloom periods, respectively. These results provide new insights on the potential control of jellyfish populations and on jellyfish importance as a food source for exploited fishes.

One-locus-several-primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies

In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in vivo evaluation using fecal and spider web samples from different invertivores, environments, and geographic locations. Our results underline the lack of predictability of both the coverage and complementarity of individual primer sets: (a) sharp discrepancies exist observed between in silico and in vivo analyses (to the detriment of in silico analyses); (b) both coverage and complementarity depend greatly on the predator and on the taxonomic level at which preys are considered; (c) primer sets' complementarity is the greatest at fine taxonomic levels (molecular operational taxonomic units [MOTUs] and variants). We then formalized the "one-locus-several-primer-sets" (OLSP) strategy, that is, the use of several primer sets that target the same locus (here the first part of the COI gene) and the same group of taxa (here invertebrates). The proximal aim of the OLSP strategy is to minimize false negatives by increasing total coverage through multiple primer sets. We illustrate that the OLSP strategy is especially relevant from this perspective since distinct variants within the same MOTUs were not equally detected across all primer sets. Furthermore, the OLSP strategy produces largely overlapping and comparable sequences, which cannot be achieved when targeting different loci. This facilitates the use of haplotypic diversity information contained within metabarcoding datasets, for example, for phylogeography and finer analyses of prey-predator interactions.

Variation in Corticosterone Levels in Two Species of Breeding Albatrosses with Divergent Life Histories: Responses to Body Condition and Drivers of Foraging Behavior

Corticosterone (CORT) is a glucocorticoid hormone that maintains energy balance and can modulate foraging behaviors in seabirds. However, CORT responses are not always predictable under similar biophysical conditions and do not necessarily influence the same behaviors across breeding stages and species. To enhance our understanding of CORT's role as a proximate determinant of foraging behavior and energy maintenance, we examined the relationships between body condition, CORT, foraging behavior, and foraging success between two sympatric breeding albatross species with differing foraging strategies and life histories, the Campbell albatross (Thalassarache impavida) and the gray-headed albatross (Thalassarache chrysostoma), from Campbell Island, New Zealand. Pre- and postforaging CORT did not differ between species or stage, potentially as a result of behavioral plasticity or different functional roles of CORT across stages. Unexpectedly, body condition did not correlate with preforaging CORT during incubation, although a negative correlation was observed in Campbell albatrosses during the guard stage. Furthermore, CORT mediated foraging success in both species and stages, but CORT mediated foraging behavior only in incubation-stage Campbell albatrosses that had shorter foraging ranges with higher pretrip CORT. Additionally, CORT positively correlated with mass gain and the time elapsed since the last feeding event in guard-stage albatrosses. Our results highlight the complexity of CORT in mediating energy balance in free-ranging animals. Our results also support that if CORT is to be usefully interpreted, breeding stage must be considered because the physiological and behavioral functionality of CORT may differ across stages, with enhanced sensitivity to energy reserves during chick rearing.

Evaluation of plant contamination in metabarcoding diet analysis of a herbivore

Fecal DNA metabarcoding is currently used in various fields of ecology to determine animal diets. Contamination of non-food DNA from complex field environments is a considerable challenge to the reliability of this method but has rarely been quantified. We evaluated plant DNA contamination by sequencing the chloroplast trnL P6 loop region from food-controlled geese feces. The average percentage of contaminant sequences per sample was 1.86%. According to the results of generalized linear models, the probability of contamination was highest in samples placed in wet soil. The proportion of contaminant sequences was lowest at the earliest sampling point and was slightly higher in samples placed in open conditions. Exclusion of rare OTUs (operational taxonomic units) was effective for obtaining reliable dietary data from the obtained sequences, and a 1% cutoff reduced the percentage of contaminated samples to less than 30%. However, appropriate interpretation of the barcoding results considering inevitable contamination is an important issue to address. We suggest the following procedures for fecal sampling and sequence data treatment to increase the reliability of DNA metabarcoding diet analyses: (i) Collect samples as soon as possible after deposition, (ii) avoid samples from deposits on wet soil, and (iii) exclude rare OTUs from diet composition estimations.

Advances in DNA Barcoding of Toxic Marine Organisms

There are more than 200,000 marine species worldwide. These include many important economic species, such as large yellow croaker, ribbonfish, tuna, and salmon, but also many potentially toxic species, such as blue-green algae, diatoms, cnidarians, ctenophores, Nassarius spp., and pufferfish. However, some edible and toxic species may look similar, and the correct identification of marine species is thus a major issue. The failure of traditional classification methods in certain species has promoted the use of DNA barcoding, which uses short, standard DNA fragments to assist with species identification. In this review, we summarize recent advances in DNA barcoding of toxic marine species such as jellyfish and pufferfish, using genes including cytochrome oxidase I gene (COI), cytochrome b gene (cytb), 16S rDNA, internal transcribed spacer (ITS), and Ribulose-1,5-bisphosphate carboxylase oxygenase gene (rbcL). We also discuss the application of this technique for improving the identification of marine species. The use of DNA barcoding can benefit the studies of biological diversity, biogeography, food safety, and the detection of both invasive and new species. However, the technique has limitations, particularly for the analysis of complex objects and the selection of standard DNA barcodes. The development of high-throughput methods may offer solutions to some of these issues.

Review: the energetic value of zooplankton and nekton species of the Southern Ocean

Understanding the energy flux through food webs is important for estimating the capacity of marine ecosystems to support stocks of living resources. The energy density of species involved in trophic energy transfer has been measured in a large number of small studies, scattered over a 40-year publication record. Here, we reviewed energy density records of Southern Ocean zooplankton, nekton and several benthic taxa, including previously unpublished data. Comparing measured taxa, energy densities were highest in myctophid fishes (ranging from 17.1 to 39.3 kJ g^-1 DW), intermediate in crustaceans (7.1 to 25.3 kJ g^-1 DW), squid (16.2 to 24.0 kJ g^-1 DW) and other fish families (14.8 to 29.9 kJ g^-1 DW), and lowest in jelly fish (10.8 to 18.0 kJ g^-1 DW), polychaetes (9.2 to 14.2 kJ g^-1 DW) and chaetognaths (5.0-11.7 kJ g^-1 DW). Data reveals differences in energy density within and between species related to size, age and other life cycle parameters. Important taxa in Antarctic food webs, such as copepods, squid and small euphausiids, remain under-sampled. The variability in energy density of Electrona antarctica was likely regional rather than seasonal, although for many species with limited data it remains difficult to disentangle regional and seasonal variability. Models are provided to estimate energy density more quickly using a species' physical parameters. It will become increasingly important to close knowledge gaps to improve the ability of bioenergetic and food web models to predict changes in the capacity of Antarctic ecosystems to support marine life.

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi-quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa-specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low-level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population-level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.

DNA barcoding reveals seasonal shifts in diet and consumption of deep-sea fishes in wedge-tailed shearwaters

The foraging ecology of pelagic seabirds is difficult to characterize because of their large foraging areas. In the face of this difficulty, DNA metabarcoding may be a useful approach to analyze diet compositions and foraging behaviors. Using this approach, we investigated the diet composition and its seasonal variation of a common seabird species on the Ogasawara Islands, Japan: the wedge-tailed shearwater Ardenna pacifica. We collected fecal samples during the prebreeding (N = 73) and rearing (N = 96) periods. The diet composition of wedge-tailed shearwater was analyzed by Ion Torrent sequencing using two universal polymerase chain reaction primers for the 12S and 16S mitochondrial DNA regions that targeted vertebrates and mollusks, respectively. The results of a BLAST search of obtained sequences detected 31 and 1 vertebrate and mollusk taxa, respectively. The results of the diet composition analysis showed that wedge-tailed shearwaters frequently consumed deep-sea fishes throughout the sampling season, indicating the importance of these fishes as a stable food resource. However, there was a marked seasonal shift in diet, which may reflect seasonal changes in food resource availability and wedge-tailed shearwater foraging behavior. The collected data regarding the shearwater diet may be useful for in situ conservation efforts. Future research that combines DNA metabarcoding with other tools, such as data logging, may provide further insight into the foraging ecology of pelagic seabirds.

Trophic signatures of seabirds suggest shifts in oceanic ecosystems

Pelagic ecosystems are dynamic ocean regions whose immense natural capital is affected by climate change, pollution, and commercial fisheries. Trophic level-based indicators derived from fishery catch data may reveal the food web status of these systems, but the utility of these metrics has been debated because of targeting bias in fisheries catch. We analyze a unique, fishery-independent data set of North Pacific seabird tissues to inform ecosystem trends over 13 decades (1890s to 2010s). Trophic position declined broadly in five of eight species sampled, indicating a long-term shift from higher-trophic level to lower-trophic level prey. No species increased their trophic position. Given species prey preferences, Bayesian diet reconstructions suggest a shift from fishes to squids, a result consistent with both catch reports and ecosystem models. Machine learning models further reveal that trophic position trends have a complex set of drivers including climate, commercial fisheries, and ecomorphology. Our results show that multiple species of fish-consuming seabirds may track the complex changes occurring in marine ecosystems.

Species-specific crab predation on the hydrozoan clinging jellyfish Gonionemus sp. (Cnidaria, Hydrozoa), subsequent crab mortality, and possible ecological consequences

Here we report a unique trophic interaction between the cryptogenic and sometimes highly toxic hydrozoan clinging jellyfish Gonionemus sp. and the spider crab Libinia dubia. We assessed species-specific predation on the Gonionemus medusae by crabs found in eelgrass meadows in Massachusetts, USA. The native spider crab species L. dubia consumed Gonionemus medusae, often enthusiastically, but the invasive green crab Carcinus maenus avoided consumption in all trials. One out of two blue crabs (Callinectes sapidus) also consumed Gonionemus, but this species was too rare in our study system to evaluate further. Libinia crabs could consume up to 30 jellyfish, which was the maximum jellyfish density treatment in our experiments, over a 24-hour period. Gonionemus consumption was associated with Libinia mortality. Spider crab mortality increased with Gonionemus consumption, and 100% of spider crabs tested died within 24 h of consuming jellyfish in our maximum jellyfish density containers. As the numbers of Gonionemus medusae used in our experiments likely underestimate the number of medusae that could be encountered by spider crabs over a 24-hour period in the field, we expect that Gonionemus may be having a negative effect on natural Libinia populations. Furthermore, given that Libinia overlaps in habitat and resource use with Carcinus, which avoids Gonionemus consumption, Carcinus populations could be indirectly benefiting from this unusual crab-jellyfish trophic relationship.